#		biogem	description	by	cite	status	version	released	issues	source	commit	dl*)	90d*)
1		bio	Bioinformatics library (...)	BioRuby project			1.4.2	6 months	5			15342	1681
2		bio gem	Biogem is a software generator for Ruby in bioinformatics (...)	Raoul J.P. Bonnal, Pjotr Prins			1.2.2	6 days	1			3533	996
3		bio gff3	Gff3 parser for big data (...)	Pjotr Prins			0.8.7	6 months	0			3020	489
4		genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom			0.0.0.4	2 years	...			2135	182
5		bio samtools	Binder of samtools for Ruby, on the top of ffi (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal			0.5.1	5 days	3			2026	832
6		bio graphics	Library for visualizing genomic regions (...)	Jan Aerts			1.4	4 years	...			1930	178
7		bio ucsc api	The Ruby ucsc api: accessing the ucsc genome database using Ruby (...)	Hiroyuki Mishima, Jan Aerts			0.3.1	5 months	1			1617	524
8		bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi			0.1.0	13 months	0			1610	246
9		intermine	Webservice client library for intermine data-warehouses (...)	Alex Kalderimis			0.99.03	5 weeks	...			1581	686
10		bio logger	Log4r wrapper with extra features for roles and sane error handling (...)	Pjotr Prins			1.0.0	6 months	0			1507	283
11		eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri			0.2.0	10 months	0			1459	190
12		ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi			1.0.1	14 months	3			1428	143
13		scaffolder	Genome scaffolding for human beings (...)	Michael Barton			0.4.4	6 months	0			1381	214
14		bio blastxmlparser	Very fast blast xml parser and library for big data (...)	Pjotr Prins			1.0.1	6 months	0			869	254
15		bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal			0.1.0	13 months	0			833	121
16		bio isoelectric point	A BioRuby plugin for calculating the isoelectric point and the charge of a protein sequence (...)	George Githinji, Pascal Betz			0.1.1	12 months	0			819	123
17		bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi			0.2.2	10 months	0			675	180
18		bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima			0.1.2	10 months	0			650	178
19		bio octopus	Running and parsing of the protein transmembrane domain predictor octopus (...)	Ben J Woodcroft			0.1.1	9 months	0			592	165
20		bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans			0.9.4	11 weeks	0			587	331
21		dna sequence aligner	Does high pairwise alignment of sequencing reads with a template (...)	John T. Prince			0.0.2	2 years	...			556	50
22		bio lazyblastxml	A plugin that allows you to parse large blast xml output files lazily, reading only what you need (...)	robsyme			0.4.0	8 months	0			551	167
23		bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam			1.0.0	5 months	1			547	172
24		bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha sequence tags (...)	George Githinji			0.5.1	2 days	0			485	239
25		bio hello	Hello world plugin for the BioRuby (just for fun :-) (...)	Toshiaki Katayama			0.0.0	13 months	0			437	62
26		bio tm hmm	A BioRuby plugin for interaction with the transmembrane predictor tmhmm (...)	Ben J. Woodcroft			0.2.0	10 months	0			425	112
27		bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama			0.0.0	14 months	0			425	63
28		bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, bwa, samtools (...)	Raoul J.P. Bonnal			0.0.1	5 months	0			344	123
29		bio signalp	A wrapper for the signal peptide prediction algorith signalp (...)	Ben J Woodcroft			0.2.0	6 weeks	0			272	142
30		bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal prediction software (...)	Ben J. Woodcroft			0.1.0	12 months	0			235	60
31		bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of translations done by the emboss bioinformatics package program transeq (...)	Ben J Woodcroft			0.1.0	10 months	0			226	56
32		bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins			0.5.1	10 weeks	0			226	159
33		bio bigbio	Low memory sequence emitters (...)	Pjotr Prins		new	0.1.4	2 weeks	0			219	219
34		intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis			0.98.1	6 months	...			182	50
35		bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins		new	0.0.4	2 weeks	3			176	176
36		bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom			1.109.0	5 months	0			173	63
37		bio core ext	BioRuby core ext: plugins which require external library or tools so are not pure Ruby plugins (...)	Raoul J.P. Bonnal, Pjotr Prins			0.0.1	5 months	0			171	63
38		bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom			1.0.0	5 months	0			170	60
39		bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal			0.1.0	5 months	0			159	62
40		bio faster	A fast parser for fasta and fastq files (...)	Francesco Strozzi			0.2.1	7 weeks	0			158	158
41		bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft			0.0.2	6 weeks	0			157	157
42		bio foo	One-line summary of your gem (...)	Toshiaki Katayama			0.0.0	3 months	0			136	64
43		bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima			0.1.1	3 months	0			133	63
44		bio wolf psort wrapper	Enables the localisation predictor wolf psort to be run locally (...)	Ben J Woodcroft		new	0.0.3	4 weeks	0			123	123
45		bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi			1.1.0	11 weeks	0			107	63
46		bio exportpred	Wrapper around the exportpred algorithm for predicting p. falciparum exported proteins (...)	Ben J Woodcroft		new	0.0.1	4 weeks	0			64	64
47		bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft		new	0.0.1	3 weeks	0			61	61
48		bio aliphatic index	A simple biogem that allows computation of the aliphatic index of a protein (...)	Ben J Woodcroft		new	0.0.1	3 weeks	0			60	60
49		bio ngs	(...)			pre	pre		...			35	27
50		bio qtlHD	(...)			pre	pre		...			19	13

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